We have investigated the usefulness of an active stabilizing system to reduce ship rolling under disturbances, using varying reaction of the flaps. In the proposed anti-rolling system for a ship, the flaps, as the actuator, are installed on the stern, in order to reject the rolling motion induced by disturbances, such as waves. The action induced by the flaps, which is dependent upon the power of the disturbances, can keep the ship in balance. In this study, we define the system parameters under the given system structure, using spectral analysis and experimental studies. Based on this information, we design the controller to evaluate the usefulness of the proposed system.